TY - JOUR
AB - Background:
The distance between two genomes is often computed by comparing only the common markers between them. Some approaches are also able to deal with non-common markers, allowing the insertion or the deletion of such markers. In these models, a deletion and a subsequent insertion that occur at the same position of the genome count for two sorting steps.
Results:
Here we propose a new model that sorts non-common markers with substitutions, which are more powerful operations that comprehend insertions and deletions. A deletion and an insertion that occur at the same position of the genome can be modeled as a substitution, counting for a single sorting step.
Conclusions:
Comparing genomes with unequal content, but without duplicated markers, we give a linear time algorithm to compute the genomic distance considering substitutions and double-cut-and-join (DCJ) operations. This model provides a parsimonious genomic distance to handle genomes free of duplicated markers, that is in practice a lower bound to the real genomic distances. The method could also be used to refine orthology assignments, since in some cases a substitution could actually correspond to an unannotated orthology.
AU - Dias Vieira Braga, MarĂlia
AU - Machado, Raphael
AU - Ribeiro, Leonardo C.
AU - Stoye, Jens
ID - 2396509
IS - Suppl 9: Proc. of RECOMB-CG 2011
JF - BMC Bioinformatics
TI - Genomic distance under gene substitutions
VL - 12
ER -